In SW, do you have Options -> External References -> "Don't prompt to save read-only referenced documents" unchecked? This will solve any issues with files that are checked in.

SW loves to modify files. If you open a file and rotate it one degree, as far as SW is concerned that file has been modified. Another common example is that if the part has any external references, and SW double checkes to ensure that reference is updated, will usually make the file "dirty"